The invention discloses palladium protamine nano particles and a preparation method thereof. The preparation method comprises the following steps: mixing proper amount of palladium salt and proper amount of protamine; stirring at certain temperature for certain time; centrifuging, separating and washing; and drying to obtain corresponding palladium salt-protamine nano particles. The preparation process is simple, the cost is low, the equipment investment is low and the preparation method is suitable for large-batch production. The preparation of the palladium salt-protamine nano particles is successfully realized, and the size of grain diameters is effectively regulated and controlled, so that the palladium protamine nano particles with the uniform grain diameters are obtained and have an excellent physicochemical property. A catalytic performance research shows that the palladium salt-protamine nano particles prepared by the method are used as a catalyst and have good catalytic activity; and the yield is more than 90% and the performance is stable, so that the nano particles have a wide application prospect in the field of catalysis.